The gut microbiota is believed to have a major impact on human health and disease. It is involved in barrier functions and maintenance of homeostasis. It provides nutrients and metabolites, participates in a signaling network, regulates epithelial development, and influences the immune system as well as protects the intestinal mucosa from the aggression of pathogenic microorganisms. There is growing evidence that physical activity has an impact on the gut microbiota. Recent studies in animals and humans suggest that regular physical activity increases the presence of beneficial microbial species and improves host health. However, some specific differences should be noted: different forms of physical activity, frequency or intensity, aerobic or resistance training, and benefits and consequences for amateur or competitive athletes. Because the positive role of physical activity can have an impact on health and various types of diseases, the results of research studies in this area are increasingly becoming the focus of scientific interest. In addition, probiotic supplements modulate intestinal microbial flora, and the ability of probiotics to modulate perturbations in immune function after exercise highlights their potential for use in individuals exposed to high levels of physical activity.